Variant report

Variant	rs11985274
Chromosome Location	chr8:20132201-20132202
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr8:20131688-20132285	U2OS	brain:	n/a	n/a
2	NFYB	chr8:20132014-20132284	K562	blood:	n/a	n/a
3	POLR2A	chr8:20131828-20132491	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:20130931..20132750-chr8:20158431..20160152,2	K562	blood:
2	chr8:20130022..20131576-chr8:20131676..20133192,2	MCF-7	breast:

Variant related genes	Relation type
LZTS1-AS1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11995187	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542827	0.90[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56256118	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57092179	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60124846	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60828034	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62499971	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62499972	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62499973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62499974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62499975	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62499976	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62499980	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62499981	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62499982	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033511	chr8:19751299-20625091	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv530877	chr8:19873053-20593254	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11985274	PEBP4	cis	cerebellum	SCAN
rs11985274	INTS10	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:20120600-20132800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr8:20126400-20132400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:20126600-20132400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:20126600-20132600	Enhancers	Placenta	Placenta
5	chr8:20126600-20135200	Weak transcription	Right Ventricle	heart
6	chr8:20126600-20136200	Enhancers	Fetal Thymus	thymus
7	chr8:20126800-20135200	Weak transcription	Lung	lung
8	chr8:20126800-20135200	Weak transcription	Right Atrium	heart
9	chr8:20126800-20135400	Weak transcription	Left Ventricle	heart
10	chr8:20127600-20134400	Weak transcription	Fetal Intestine Small	intestine
11	chr8:20129000-20133000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr8:20129000-20133200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr8:20129600-20133400	Enhancers	Fetal Muscle Trunk	muscle
14	chr8:20129600-20135400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr8:20129600-20137800	Weak transcription	Fetal Intestine Large	intestine
16	chr8:20129600-20139400	Weak transcription	NH-A	brain
17	chr8:20129800-20133000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr8:20129800-20136400	Enhancers	NHDF-Ad	bronchial
19	chr8:20130000-20132400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:20130200-20132400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr8:20130200-20133000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr8:20130400-20132400	Genic enhancers	HSMM	muscle
23	chr8:20130400-20132600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr8:20130400-20135200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:20130600-20132400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr8:20130600-20133000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr8:20130800-20132400	Enhancers	NHLF	lung
28	chr8:20131000-20132400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr8:20131000-20135000	Weak transcription	Fetal Brain Female	brain
30	chr8:20131000-20135200	Weak transcription	Spleen	Spleen
31	chr8:20131000-20135400	Weak transcription	Brain Anterior Caudate	brain
32	chr8:20131000-20136600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr8:20131200-20133000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr8:20131200-20133200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr8:20131200-20133200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr8:20131200-20134000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr8:20131200-20135400	Enhancers	Fetal Muscle Leg	muscle
38	chr8:20131200-20137600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr8:20131600-20132600	Flanking Active TSS	Dnd41	blood
40	chr8:20131600-20136400	Enhancers	Primary T cells from cord blood	blood
41	chr8:20131800-20132400	Enhancers	H9 Cell Line	embryonic stem cell
42	chr8:20131800-20132600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr8:20131800-20133000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr8:20131800-20133200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr8:20131800-20133800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr8:20132000-20132400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr8:20132000-20133200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr8:20132000-20133600	Genic enhancers	HSMMtube	muscle
49	chr8:20132000-20134600	Weak transcription	Fetal Lung	lung
50	chr8:20132000-20136000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links